Ah very good, thanks
So only the latex problem seems to be still quite strange. After updating every single LaTeX program on my Mac, it still has the same problem. I think, it might be an El Capitan problem, if you look at all the issues they seem to have with it:
*Users updating from Yosemite to El Capitan may encounter one problem with TeX, but it is easily fixed. After that, MacTeX works fine on Apple's latest operating system.
MacTeX installs a symbolic link /usr/texbin pointing to the TeX binaries. GUI applications use this link to find the binaries. But in El Capitan, the location /usr is reserved for Apple, and even users with root access are not allowed to write to that location.
The solution to this problem is to relocate the link to /Library/TeX/texbin, and reconfigure GUI applications to look in this location. Consequently, MacTeX-2015 and BasicTeX-2015 write two links, /usr/texbin and /Library/TeX/texbin, when installing on systems earlier than El Capitan, and write /Library/TeX/texbin when installing on El Capitan. These installations configure shell applications to look for TeX in both locations.
Consequently, if you install MacTeX-2015 or BasicTeX-2015 after upgrading to El Capitan, or if you have already installed one of them before upgrading, then TeX will work as usual when accessed from the Terminal, and will work from GUI applications once these are reconfigured.
The latest version of TeXShop automatically reconfigures itself. This version was released a month after MacTeX-2015 was released, so TeXShop users should use the menu item "Check for Updates" before using it on El Capitan.
Herbert Schulz's document Updating For El Capitan carefully explains how to update the other GUI applications installed by MacTeX, and how to update a few other popular applications.
The new symbolic links also work for older TeX installations. Once they are installed by MacTeX-2015 or BasicTeX-2015 and GUI applications are reconfigured, users can switch back to, say, TeXLive-2013 using the TeX Distribution Preference Pane as usual. Users who don't want to install one of the 2015 distributions can write the new links directly using instructions in Herbert Schulz's document.*